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- EMDB-13478: Vault structure in primmed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-13478
TitleVault structure in primmed conformation
Map data
Sample
  • Cell: major vault protein from Rattus norvegicus
    • Protein or peptide: Major vault protein
Function / homology
Function and homology information


protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / Neutrophil degranulation / negative regulation of epidermal growth factor receptor signaling pathway / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain ...Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGuerra P / Gonzalez-Alamos M / Llauro A / Casanas A / Querol-Audi J / de Pablo P / Verdaguer N
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish National Research Council20202CEX003 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-83906-P Spain
CitationJournal: Sci Adv / Year: 2022
Title: Symmetry disruption commits vault particles to disassembly.
Authors: Pablo Guerra / María González-Alamos / Aida Llauró / Arnau Casañas / Jordi Querol-Audí / Pedro J de Pablo / Núria Verdaguer /
Abstract: Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is ...Vaults are ubiquitous ribonucleoprotein particles involved in a diversity of cellular processes, with promising applications as nanodevices for delivery of multiple cargos. The vault shell is assembled by the symmetrical association of multiple copies of the major vault protein that, initially, generates half vaults. The pairwise, anti-parallel association of two half vaults produces whole vaults. Here, using a combination of vault recombinant reconstitution and structural techniques, we characterized the molecular determinants for the vault opening process. This process commences with a relaxation of the vault waist, causing the expansion of the inner cavity. Then, local disengagement of amino-terminal domains at the vault midsection seeds a conformational change that leads to the aperture, facilitating access to the inner cavity where cargo is hosted. These results inform a hitherto uncharacterized step of the vault cycle and will aid current engineering efforts leveraging vault for tailored cargo delivery.
History
DepositionAug 26, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pkr
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pkr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13478.png

Downloads & links

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Map

FileDownload / File: emd_13478.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.69 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.14411601 - 0.18043189
Average (Standard dev.)0.0007472293 (±0.009465116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 676.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z676.000676.000676.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1440.1800.001

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Supplemental data

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Sample components

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Entire : major vault protein from Rattus norvegicus

EntireName: major vault protein from Rattus norvegicus
Components
  • Cell: major vault protein from Rattus norvegicus
    • Protein or peptide: Major vault protein

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Supramolecule #1: major vault protein from Rattus norvegicus

SupramoleculeName: major vault protein from Rattus norvegicus / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Major vault protein

MacromoleculeName: Major vault protein / type: protein_or_peptide / ID: 1 / Number of copies: 78 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.920109 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATEEAIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPVRM VTVPPRHYCI VANPVSRDTQ SSVLFDITGQ VRLRHADQE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKNGDKVMA GDEWLFEGPG TYIPQKEVEV V EIIQATVI ...String:
MATEEAIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPVRM VTVPPRHYCI VANPVSRDTQ SSVLFDITGQ VRLRHADQE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKNGDKVMA GDEWLFEGPG TYIPQKEVEV V EIIQATVI KQNQALRLRA RKECFDREGK GRVTGEEWLV RSVGAYLPAV FEEVLDLVDA VILTEKTALH LRALQNFRDL RG VLHRTGE EWLVTVQDTE AHVPDVYEEV LGVVPITTLG PRHYCVILDP MGPDGKNQLG QKRVVKGEKS FFLQPGERLE RGI QDVYVL SEQQGLLLKA LQPLEEGESE EKVSHQAGDC WLIRGPLEYV PSAKVEVVEE RQAIPLDQNE GIYVQDVKTG KVRA VIGST YMLTQDEVLW EKELPSGVEE LLNLGHDPLA DRGQKGTAKP LQPSAPRNKT RVVSYRVPHN AAVQVYDYRA KRARV VFGP ELVTLDPEEQ FTVLSLSAGR PKRPHARRAL CLLLGPDFFT DVITIETADH ARLQLQLAYN WHFELKNRND PAEAAK LFS VPDFVGDACK AIASRVRGAV ASVTFDDFHK NSARIIRMAV FGFEMSEDTG PDGTLLPKAR DQAVFPQNGL VVSSVDV QS VEPVDQRTRD ALQRSVQLAI EITTNSQEAA AKHEAQRLEQ EARGRLERQK ILDQSEAEKA RKELLELEAM SMAVESTG N AKAEAESRAE AARIEGEGSV LQAKLKAQAL AIETEAELER VKKVREMELI YARAQLELEV SKAQQLANVE AKKFKEMTE ALGPGTIRDL AVAGPEMQVK LLQSLGLKST LITDGSSPIN LFSTAFGLLG LGSDGQPPAQ K

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTrisTris buffer pH 7.5
75.0 mMNaClSodium chlorideSodium Chloride
1.0 mMMgCl2Magnesium Chloride
1.0 mMDTTdithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hl8

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9793

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Atomic model buiding 1

Initial modelPDB ID:

4hl8

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7pkr:
Vault structure in primmed conformation

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